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Nate Corley

@ncorley.bsky.social

PhD Candidate @ the University of Washington's Institute for Protein Design | Baker Lab | Machine Learning for Protein Design | Enzymes

Posts Replies Media

Nate Corley @ncorley.bsky.social · 19/09/2025

RFdiffusion3 is here! We train a general network that explicitly models every atom and use it to design active enzymes and DNA binders. Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others! Check it out: lnkd.in/eiUFfJaM.

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Chaitanya K. Joshi @chaitjo.bsky.social · 15/08/2025

RosettaFold 3 is here! 🧬🚀 AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release! Congratulations @simonmathis.bsky.social and team!!! ❤️ bioRxiv preprint: www.biorxiv.org/content/10.1...

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Kieran Didi @kdidi.bsky.social · 15/08/2025

`atomworks.ml` on the other hand offers advanced dataset featurization and sampling for deep learning workflows, all operating on the canonical AtomArray object from @biotite_python so that all transforms are traceable and generalizable between models. 4/6

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Kieran Didi @kdidi.bsky.social · 15/08/2025

AtomWorks has two main components: atomworks.io takes a file (cif, sdf, ...) and does parsing, cleaning and more. You can also look at your structures in a notebook or via PyMol thanks to pymol-remote, so you can directly inspect if your code does what you want! 3/6

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Kieran Didi @kdidi.bsky.social · 15/08/2025

AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`! AtomWorks: github.com/RosettaCommo... RF3: github.com/RosettaCommo... Paper: tinyurl.com/y2w4z65b 1/6

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Nate Corley @ncorley.bsky.social · 15/08/2025

(1/7) Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3) [www.biorxiv.org/content/10.1101/202…...)

biorxiv.org

Accelerating Biomolecular Modeling with AtomWorks and RF3

Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...

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